[ccp4bb] Differentiating bound Mn & Ca - Summary

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Subject: Differentiating bound Mn & Ca - Summary
From: David Briggs bassophile {- at -} GMAIL {- dot -} COM
Date: 2007-04-17

Dear all.

Thanks to all of those who replied to my question, especially Clemens
Vonrhein, who patiently helped me get SHARP up and running...

Basically, there were 4 different ways suggested, with a few
embellishments here and there.

1) Use Dano peak height.
Taking the Dano peak height for intrinsic sulphurs as a standard, you
can then estimate the f" of the unknown anomalous scatterer, and use
that to discriminate between Ca & Mn.
(In my case, Dano map was noisy below 4sig and only 2 out of 5
sulphurs had any sort of peak). (Jochen Kuper, Kay Diederichs, Remy
Loris, Eleanor)

One caveat is that the height of the Dano peak height is very B-factor
dependant - one suggested solution was to use mapman to integrate a
box/sphere around the anomalous scatterers (S and unknown) and
calculate a ration of the peak height that way, which apparently tends
to remove much of the B-factor dependence of the analysis (Stephen
Graham, Mitch Miller)

2) Use a heavy atom refinment program, such as SHARP or Phenix
xtal.refine to refine f" and/or f' values - inputting current phase
probs as HLs.

(Clemens & Peter Zwart)

3) Use Inductively coupled plasma optical emission spectroscopy (ICP-OES)
to do an elemental analysis - Mn or Ca should be very obvious

(Artem & Roger S. Rowlett)

4) atomic absorption spectroscopy
(Charlie Bond)

Other suggestions included trying to crystallise the protein in either
Mn or Ca to see if it preferentially crystallises in one or the other.

Other ideas suggested closer to home include (micro)PIXE, and intact
mass analysis - maybe.

The obvious scan around the Mn K edge is still the definitive
crystallography-based test..

Thank you very much for all your helpful suggestions.

Dave

--
---------------------------------------
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
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Anyone who is capable of getting themselves made President should on
no account be allowed to do the job. - Douglas Adams

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